[English] 日本語
Yorodumi
- PDB-1hy8: SOLUTION STRUCTURE OF B. SUBTILIS ACYL CARRIER PROTEIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1hy8
TitleSOLUTION STRUCTURE OF B. SUBTILIS ACYL CARRIER PROTEIN
ComponentsACYL CARRIER PROTEIN
KeywordsLIPID BINDING PROTEIN / apo-ACP / holo-ACP / ACPS / Fatty Acid Biosynthesis / 4' phosphopantetheine prosthetic group
Function / homology
Function and homology information


lipid A biosynthetic process / acyl binding / acyl carrier activity / cytosol
Similarity search - Function
ACP-like / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Acyl carrier protein (ACP) / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Acyl carrier protein
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / Distance geometry, Simulated annealing, molecular dynamics
AuthorsXu, G.-Y. / Tam, A. / Lin, L. / Hixon, J. / Fritz, C.C. / Power, R.
CitationJournal: Structure / Year: 2001
Title: Solution structure of B. subtilis acyl carrier protein.
Authors: Xu, G.Y. / Tam, A. / Lin, L. / Hixon, J. / Fritz, C.C. / Powers, R.
History
DepositionJan 18, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ACYL CARRIER PROTEIN


Theoretical massNumber of molelcules
Total (without water)8,4661
Polymers8,4661
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representative

-
Components

#1: Protein ACYL CARRIER PROTEIN / ACP


Mass: 8466.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: PGEX-6P-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P80643

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 3D 15N-separated NOESY
NMR detailsText: This structure was determinined using 3D triple-resonance experiments with the enhanced-sensitivity pulse field gradient approach, simultaneous 15N/13C-edited NOESY and 2D constant time 13C-1H HSQC techniques.

-
Sample preparation

DetailsContents: 1mM sample is the mixture of U-15N/13C labeled holo- (60%)and apo-ACP (40%)
Solvent system: 50 mM Bis-Tris, 100 mM sodium chloride, 10 mM magnesium chloride and 10 mM DTT in 5% D2O, 95% H2O
Sample conditionsIonic strength: 3.4 / pH: 6.4 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
X-PLOR98Badger, J., Kumar, R.A., Yip, P.structure solution
NMRPipe1.8, 2000Delaglio, F.processing
PIPP4.2.2, 1998Garrett, D.data analysis
X-PLOR98Badger, J., Kumar, R.A., Yip, P.refinement
RefinementMethod: Distance geometry, Simulated annealing, molecular dynamics
Software ordinal: 1
Details: The structures are based on a total of 1050 distance constraints from NOE and H-bond, 96 dihedral angle constraints from Talos program and 76 pairs of CA/CB chemical shift constraints
NMR ensembleConformers submitted total number: 1

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more